cfDNAWGS2

This function is used for case/control analysis of paired/single end WGS data.

Note

User must set pipeConfigure2 before using.

Parameters

cfDNAWGS2(caseFolder=None,
          ctrlFolder=None,
          caseName=None,
          ctrlName=None,
          caseFq1=None,
          caseFq2=None,
          ctrlFq1=None,
          ctrlFq2=None,
          caseAdapter1=["AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"],
          caseAdapter2=["AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"],
          ctrlAdapter1=["AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"],
          ctrlAdapter2=["AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"],
          fastqcOP=None,
          idAdapter=True,
          idAdOP=None,
          rmAdapter=True,
          rmAdOP={"--qualitybase": 33, "--gzip": True},
          bowtie2OP={"-q": True, "-N": 1, "--time": True},
          dudup=True,
          CNV=False,
          armCNV=False,
          fragProfile=False,
          report=False,
          verbose=False,
          box=True)

  • caseFolder: str, input case fastq file folder path. Setting this parameter means disable fastq1 and fastq2.

  • ctrlFolder: str, input control fastq file folder path. Setting this parameter means disable fastq1 and fastq2.

  • caseFq1: list, case fastq1 files.

  • caseFq2: list, case fastq2 files.

  • ctrlFq1: list, control fastq1 files.

  • ctrlFq2: list, control fastq2 files.

  • caseAdapter1: list, adapters for case fastq1 files, if idAdapter is True, this paramter will be disabled.

  • caseAdapter2: list, adapters control for case fastq2 files, if idAdapter is True, this paramter will be disabled.

  • ctrlAdapter1: list, adapters control for fastq1 files, if idAdapter is True, this paramter will be disabled.

  • ctrlAdapter2: list, adapters for fastq2 files, if idAdapter is True, this paramter will be disabled.

  • fastqcOP: Other parameters used for fastqc, please see class “fastqc”.

  • idAdapter: Ture or False, identify adapters or not. This module is not for single end data.

  • idAdOP: Other parameters used for AdapterRemoval, please see class “identifyAdapter”.

    If idAdapter is False, this paramter will be disabled.

  • rmAdapter: Ture or False, remove adapters or not.

  • rmAdOP: Other parameters used for AdapterRemoval, please see class “adapterremoval”.

    Default: {“–qualitybase”: 33, “–gzip”: True}. If rmAdapter is False, this paramter will be disabled.

  • bowtie2OP: Other parameters used for Bowtie2, please see class “bowtie2”.

    Default: {“-q”: True, “-N”: 1, “–time”: True}.

  • dudup: Ture or False, remove duplicates for bowtie2 results or not.

  • CNV: Compute CNV or not. If True, CNV will be computed for 3 group: case VS reference,

    control VS reference, case VS control.

  • armCNV: Compute arm level CNV or not.

  • fragProfile: Compute basic fragProfile(long short fragement statistics) or not. This module is not for single end data.

    OCF: Compute OCF or not.

  • report: Generate user report or not.

  • verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

  • box: output will be a box class. that mean the the results can be specified using ‘.’,

    otherwise, the results will be saved as dict.

Example usage:

from cfDNApipe import *

pipeConfigure2(
    threads=60,
    genome="hg19",
    refdir="path_to_genome/hg19_bowtie2",
    outdir="path_to_output/pipeline-WGS-comp",
    data="WGS",
    type="paired",
    JavaMem="8G",
    case="cancer",
    ctrl="normal",
    build=True,
)

case, ctrl, comp = cfDNAWGS2(
    caseFolder="path_to_fastqs/raw/case",
    ctrlFolder="path_to_fastqs/raw/ctrl",
    caseName="cancer",
    ctrlName="normal",
    idAdapter=True,
    rmAdapter=True,
    rmAdOP={"--qualitybase": 33, "--gzip": True},
    bowtie2OP={"-q": True, "-N": 1, "--time": True},
    dudup=True,
    CNV=True,
    armCNV=True,
    fragProfile=True,
    OCF=True,
    report=True,
    verbose=False,
)